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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

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Related Experiment Video

Updated: May 21, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Detecting differential usage of exons from RNA-seq data.

Simon Anders1, Alejandro Reyes, Wolfgang Huber

  • 1European Molecular Biology Laboratory, 69111 Heidelberg, Germany. sanders@fs.tum.de

Genome Research
|June 23, 2012
PubMed
Summary
This summary is machine-generated.

DEXSeq is a new statistical method for analyzing RNA-seq data to detect differential exon usage. It accurately identifies genes and exons with altered expression, aiding in the study of alternative splicing regulation.

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Last Updated: May 21, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA sequencing (RNA-seq) is crucial for studying alternative splicing and isoform expression.
  • Accurate detection of differential isoform abundance is essential for understanding gene regulation across conditions.
  • Existing methods may lack the sensitivity or specificity needed for comprehensive analysis.

Purpose of the Study:

  • To introduce DEXSeq, a novel statistical method for detecting differential exon usage in RNA-seq data.
  • To provide a sensitive and specific tool for analyzing alternative splicing events.
  • To facilitate genome-wide studies on the regulation and function of alternative exon usage.

Main Methods:

  • DEXSeq employs generalized linear models to analyze RNA-seq data.
  • The method incorporates biological variation for robust control of false discoveries.
  • Statistical testing is performed at the exon level to identify differential usage.

Main Results:

  • DEXSeq demonstrates high sensitivity in detecting genes with differential exon usage.
  • The method can identify specific exons that are differentially used.
  • Application to diverse datasets showcases DEXSeq's versatility and effectiveness.

Conclusions:

  • DEXSeq offers a reliable approach for analyzing differential exon usage in RNA-seq.
  • The method enhances the study of alternative splicing regulation and function.
  • DEXSeq is available as an R/Bioconductor package for broad accessibility.